Detection of freshwater mussels (Sinanodonta spp.) in artificial ponds through environmental DNA: a comparison with traditional hand collection methods

Togaki, Daisuke; Doi, Hideyuki; Katano, Izumi

doi:10.1007/s10201-019-00584-0

Cited by 11 publications

(9 citation statements)

References 37 publications

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“…Most eDNA studies that use a filtration approach have been conducted in marine or freshwater systems, where water appears to be non-turbid at the time of collection [15][16][17][18]. This is owing to the unique set of challenges that turbid water poses when detecting eDNA, such as the clogging of filters and the presence of PCR inhibitors [19][20][21]. Previous studies have utilised extraction kits-which come with anti-inhibitory washes-various pore sizes, membrane types, and pre-filtration steps to prevent filter clogging [22][23][24][25].…”

Section: Introductionmentioning

confidence: 99%

Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding

Takasaki¹,

Aihara²,

Imanaka³

et al. 2021

PLoS ONE

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Environmental DNA (eDNA) analysis is a novel approach for biomonitoring and has been mostly used in clear water. It is difficult to detect eDNA in turbid water as filter clogging occurs, and environmental samples contain various substances that inhibit the polymerase chain reaction (PCR) and affect the accuracy of eDNA analysis. Therefore, we applied a pre-filtration method to better detect the fish species (particularly pale chub, Opsariichthys platypus) present in a water body by measuring eDNA in environmental samples containing PCR inhibitors. Upon conducting 12S rRNA metabarcoding analysis (MiFish), we found that pre-filtration did not affect the number or identities of fish species detected in our samples, but pre-filtration through pore sizes resulted in significantly reduced variance among replicate samples. Additionally, PCR amplification was improved by the pre-filtration of environmental samples containing PCR inhibitors such as humic substances. Although this study may appear to be a conservative and ancillary experiment, pre-filtration is a simple technique that can not only improve the physical properties of water, such as turbidity, but also the quality of eDNA biomonitoring.

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Section: Introductionmentioning

confidence: 99%

Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding

Takasaki¹,

Aihara²,

Imanaka³

et al. 2021

PLoS ONE

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“…Limnoperna fortunei has already been found in the water source of the study sites (Tsuchiurashigai 15-choson land improvement district: personal communication), meaning it is possible that L. fortunei had already invaded these four ponds. There are some reports that eDNA has been detected in places where the target species has not been found by conventional surveys (Thomsen et al 2012, Togaki et al 2020, suggesting a high sensitivity of eDNA survey methods. Supporting this view, these four ponds had lower eDNA concentrations than the sites where the presence of L. fortunei was confirmed by conventional surveys (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…These studies, however, provide little information on the relationship between L. fortunei abundance and field eDNA concentrations. In order to use eDNA in field surveys of organisms, it is important to compare its effectiveness to that of conventional census methods (Roussel et al 2015, Togaki et al 2020, Tréguier et al 2014.…”

Section: Introductionmentioning

confidence: 99%

Use of environmental DNA to survey the distribution of the invasive mussel <i>Limnoperna fortunei</i> in farm ponds

Ito

Shibaike

2021

Plankton Benthos Res

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The golden mussel Limnoperna fortunei (Dunker, 1857) is an invasive freshwater bivalve species that exerts harmful effects on the environment, as well as man-made structures, such as water-treatment systems. By using conventional sampling methods, it is difficult to detect mussels under low-density conditions; however, environmental DNA (eDNA) analysis may be a rapid and efficient method for monitoring this aquatic organism. In this study, we conducted surveys based on the eDNA analysis of L. fortunei in 15 farm ponds in Japan and compared the results with those of two conventional survey methods, visual census and plankton larval survey, to clarify the effectiveness of eDNA analysis for field surveys of L. fortunei. Primers and a probe specific to L. fortunei were developed, and a method for analysis was established. In the laboratory experiments, the species eDNA was detected in all water tanks containing the mussels, and the concentration of eDNA was high in the experimental tank that had high density of L. fortunei. In the field survey, L. fortunei eDNA was detected in all ponds where the mussels were found by conventional survey, and low concentrations of eDNA were also detected in several ponds where no L. fortunei were found by traditional methods. These results suggest that eDNA analysis has greater sensitivity for the detection of L. fortunei in farm ponds than that of conventional methods. Environmental DNA surveys have little impact on water management and are suitable for surveys at water facilities that have not yet been damaged by the mussels.

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“…The assays described here will be particularly useful for assessing presence of freshwater mussel populations in locations with suitable habitat, or where populations have been previously described, with costs far lower than traditional stream or river-bed surveys (Stoeckle et al 2016, Togaki et al 2019. Further, our assays could be used in systematic monitoring programs to detect life history events such as glochidial releases or mussels die-offs, both of which would be expected to show dramatic increases in eDNA concentrations.…”

Section: Discussionmentioning

confidence: 99%

Detection of 4 imperiled western North American freshwater mussel species from environmental DNA with multiplex qPCR assays

et al. 2020

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We developed multiplexed, species-specific, quantitative PCR assays for the detection of four freshwater mussel species native to western North America, Gonidea angulata, Margaritifera falcata, Anodonta nuttalliana and Anodonta oregonensis, from environmental DNA (eDNA). These species have experienced dramatic declines over the last century and are currently threatened in many portions of their ranges. Therefore, improved tools for detecting and monitoring these species are needed. Speciesspecificity and sensitivity of assays were empirically tested in the lab, and multiplex assays were also validated with field collected eDNA samples. All assays were species-specific, sensitive, and effective for detection from eDNA samples collected from streams and rivers. These assays will aid in the detection, monitoring, management, and conservation of these vulnerable species.

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Detection of freshwater mussels (Sinanodonta spp.) in artificial ponds through environmental DNA: a comparison with traditional hand collection methods

Cited by 11 publications

References 37 publications

Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding

Water pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding

Use of environmental DNA to survey the distribution of the invasive mussel <i>Limnoperna fortunei</i> in farm ponds

Detection of 4 imperiled western North American freshwater mussel species from environmental DNA with multiplex qPCR assays

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